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- PDB-4gq0: Crystal structure of AKR1B10 complexed with NADP+ and Caffeic aci... -

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Basic information

Entry
Database: PDB / ID: 4gq0
TitleCrystal structure of AKR1B10 complexed with NADP+ and Caffeic acid phenethyl ester
ComponentsAldo-keto reductase family 1 member B10
KeywordsOXIDOREDUCTASE / alpha-beta TIM barrel / NADP-dependant oxidoreductase / Caffeic acid phenethyl ester and NADP+
Function / homology
Function and homology information


indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADP) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / NADP-retinol dehydrogenase activity ...indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADP) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / NADP-retinol dehydrogenase activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / retinoid metabolic process / alditol:NADP+ 1-oxidoreductase activity / Retinoid metabolism and transport / lysosome / mitochondrion / extracellular region / cytosol
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-QAP / Aldo-keto reductase family 1 member B10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiping, Z. / Xuehua, Z. / Shangke, C. / Jing, Z. / Xiaopeng, H.
CitationJournal: To be Published
Title: Crystal structure of AKR1B10 complexed with NADP+ and Caffeic acid phenethyl ester
Authors: Liping, Z. / Xuehua, Z. / Shangke, C. / Jing, Z.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
SupersessionDec 4, 2013ID: 3V9Q
Revision 1.1Dec 4, 2013Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member B10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3253
Polymers36,2981
Non-polymers1,0282
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.593, 90.593, 78.372
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Aldo-keto reductase family 1 member B10 / ARL-1 / Aldose reductase-like / Aldose reductase-related protein / ARP / hARP / Small intestine ...ARL-1 / Aldose reductase-like / Aldose reductase-related protein / ARP / hARP / Small intestine reductase / SI reductase


Mass: 36297.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: AKR1B10 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21
References: UniProt: O60218, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-QAP / 2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate / Caffeic acid phenethyl ester


Mass: 284.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16O4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE CORRESPONDS TO VARIANT RS4728329.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100mM Tris, 30-35% PEG6000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 21, 2012
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→24.8 Å / Num. all: 21351 / Num. obs: 21323 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.067 / Net I/σ(I): 16.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3033 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZUA
Resolution: 2.1→23.646 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8495 / SU ML: 0.27 / σ(F): 1.79 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1097 5.14 %random
Rwork0.1737 ---
all0.1779 21323 --
obs0.1764 20505 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.788 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 80.75 Å2 / Biso mean: 28.7039 Å2 / Biso min: 7.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.2292 Å20 Å2-0 Å2
2--0.2292 Å20 Å2
3----0.1751 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 69 183 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082707
X-RAY DIFFRACTIONf_angle_d1.1733675
X-RAY DIFFRACTIONf_chiral_restr0.076398
X-RAY DIFFRACTIONf_plane_restr0.006477
X-RAY DIFFRACTIONf_dihedral_angle_d16.0831030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.19550.29511570.22432436259398
2.1955-2.31120.32341180.239425422660100
2.3112-2.45580.24171320.203825232655100
2.4558-2.64520.26751370.197225192656100
2.6452-2.9110.2491470.190125272674100
2.911-3.33120.21461330.182925482681100
3.3312-4.19320.19831520.149225272679100
4.1932-23.64760.18181210.137426042725100

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